Best Peak Caller For Histone Modifications (Mainly H3K4Me3) Chip-Seq Datasets?

Question

[2184687-1231-83-]

I've heard of MACS for peak/region calling of histone modification chip-seq datasets (mainly H3K4me3), but I am wondering if there is any other tool I should consider as well.

[Mikael Huss]

This BioStar thread is similar.

Answer 1

[Mikael Huss]

SICER is especially designed for histone marks. The recently published PeakRanger also does diffuse profiles (like histone marks) and seems interesting.

[endrebak]

New version of SICER: https://github.com/endrebak/epic

Answer 2

[Dataminer]

MACS is best although you can try PICS as well.

Reason for using PICS: Two binding sites are separated into two disjoint regions by PICS, whereas MACS combines these two sites into a single region. This makes PICS particularly attractive for subsequent motif based analysis.

:)

[2184687-1231-83-]

"Best" in terms of "user experience": having first-hand experience with your own data and liking one as the best in comparison to others.

[Ian]

Personal experience shows that MACS is not good for histones. But excellent for TFs, although not terribly sensitive.

[Mikael Huss]

MACS is best, based on what criterion?

[Dataminer]

Personally no algorithm is based, it was my personal biased opinion. Although I also gave a second option of PICS and guess you are big fan of SICER .. :)

[Dataminer]

Personally no algorithm is best, it was my personal biased opinion. I also gave a second option of PICS and I guess you are a big fan of SICER .. :)

[Mikael Huss]

Haven't used SICER much really, but it does have an underlying model of histone mark enrichment (based on nucleosome spacing). CCAT is the package I've used the most for histone modifications

[Dataminer]

@avilella: Well said

[Mikael Huss]

Sorry for being grumpy ... I guess what I was trying to say was that the answer did not address the issue of how MACS and PICS are addressing histone modification profiles specifically. This is a scenario where motif based analysis (as you suggested for PICS) is not very relevant.

[Dataminer]

Its ok Mikael, once in a while we all are grumpy :) To be honest no algorithm is perfect (as far as I know) they all have drawbacks. I agree that SICER could be a better choice depending upon what kind of biological question you want to address after marking the histone modification profiles. And, I never said you were wrong and I was right.

Friends?

Answer 3

[Ian]

I have not had chance to look at this yet, but RSEG looks very promising! I expect this to be good as Andrew Smith has historically produced very useful software tools, e.g. CREAD and DME.

We have also had a good experience using SICER.

Although i routinely use MACS for ChIP-seq i would not recommend its use with histone data.

Answer 4

[Benm]

Maybe you can find the answer from this article: Shirley Pepke, Barbara Wold & Ali Mortazavi, Computation for ChIP-seq and RNA-seq studies. Nature Methods 6, S22 - S32 (2009).

And this question had been discussed in SEQanswers before, just try to google "ChIP-Seq Challenge".

[2184687-1231-83-]

It would be great to be able to pull SEQanswers content in the "Related questions" area in Biostar.

Answer 5

[Casey Bergman]

I have not tried this myself, but you can have a look at the ChipSeqR Bioconductor package. There is a fairly extensive section on testing this method in the associated paper by Humburg et al. that may get to the issue of "best" peak caller for nucleosomes/histon modifications. This paper also cites two other papers by Albert et al and Kharchenko et al that are probably worth having a look at as well.